These tutorials explain steps that are used to analyze real-world sequencing data. We will try to explain the steps in detail but command output are usually ignored for brevity and confidentiality reasons.

1.  Quick Start Guide

This is a 10-minute quick start guide using data from the 1000 genomes project. We encourage you to walk through this minimal real-world example to get a feel for the software and assess its helpfulness.

2.  Presentations

3.  Introductory tutorials

  • A recent presentation about variant tools, with output of commands
  • A tutorial session in the ACM BCB 2014 meeting

4.  Variants screening

  • Analyzing 44 whole genome cases and 200 exome controls, with detailed performance measures
  • Analyzing 5 whole-genome samples from Illumina
  • Compare variants from the same samples called by Complete Genomics and Illumina
  • Select variants belonging to specified genes
  • Detailed analysis of one variant

5.  Import and export

  • Import all genotype data from the 1000 genomes project
  • Generate and import annovar annotations for variants already in vtools
  • Import variants from a list of variants in an unsupported format
  • Handling genotypes imported from multiple files (e.g. genotypes of samples are imported chromosome by chromosome)

6.  Reference genomes and annotation databases

  • Working with mouse and other genomes

7.  Annotation

  • Annotating variants using multiple annotation databases

8.  Association analysis

  • Quality control using sequencing data
  • Association analysis using sequencing data

9.  Parallelization

  • Use subprojects to manage large projects. This strategy can be used to parallelize variant processing using multiple processors or a cluster